I've been trying to make a simple app using visual studio express to do this without much success. However, after playing around with graphedit I have found something that may be useful for people with ATI hardware (I'm not sure if my ATI Theatre 650 installed these filters, or my HD3200).
This graph takes the mpeg streams from the source .wtv file and remuxes them into a new mpeg file. I haven't tried the resulting file with any software other than VLC and WindowsMediaPlayer11 yet.
note: The audio and video pins change depending on the source recording
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1. Graph->Insert Filters->DiectShow Filters->StreamBufferSource. Select source file.
Graph->Insert Filters->DiectShow Filters->ATI MPEG Multiplexer
Graph->Insert Filters->DiectShow Filters->ATI MPEG File Writer. Select output file.
2. Right-Click on each pin from the StreamBufferSource and select "Render Pin" until the 1 audio and 1 video pin are connected to the ATI MPEG Multiplexer. The other connections will be made automatically.
3. Delete any filters that may be connected to any pins that are not your uadio and video pins (in case you rendered any extra pins while trying to find the audio and video pins).
4. Click on the "Play" button.
On my machine this created a new file very quickly (3 min for a 1 1/2 hour hd recording). No processing or transcoding going on, just repackaging the A/V data.
I hope this can help put some people on the right track.